diff --git a/docs/abci-cli.md b/docs/abci-cli.md
index 14095d16..e6ae0037 100644
--- a/docs/abci-cli.md
+++ b/docs/abci-cli.md
@@ -125,7 +125,7 @@ response.
 The server may be generic for a particular language, and we provide a
 [reference implementation in
 Golang](https://github.com/tendermint/abci/tree/master/server). See the
-[list of other ABCI implementations](./ecosystem.html) for servers in
+[list of other ABCI implementations](./ecosystem.md) for servers in
 other languages.
 
 The handler is specific to the application, and may be arbitrary, so
@@ -324,6 +324,6 @@ connects to the app using three separate connections, each with its own
 pattern of messages.
 
 For more information, see the [application developers
-guide](./app-development.html). For examples of running an ABCI app with
-Tendermint, see the [getting started guide](./getting-started.html).
+guide](./app-development.md). For examples of running an ABCI app with
+Tendermint, see the [getting started guide](./getting-started.md).
 Next is the ABCI specification.
diff --git a/docs/deploy-testnets.md b/docs/deploy-testnets.md
index 0c74b2c5..e5b30083 100644
--- a/docs/deploy-testnets.md
+++ b/docs/deploy-testnets.md
@@ -35,7 +35,7 @@ Here are the steps to setting up a testnet manually:
 
 After a few seconds, all the nodes should connect to each other and
 start making blocks! For more information, see the Tendermint Networks
-section of [the guide to using Tendermint](using-tendermint.html).
+section of [the guide to using Tendermint](./using-tendermint.md).
 
 But wait! Steps 3 and 4 are quite manual. Instead, use [this
 script](https://github.com/tendermint/tendermint/blob/develop/docs/examples/init_testnet.sh),
diff --git a/docs/getting-started.md b/docs/getting-started.md
index 9767dae5..aa42a706 100644
--- a/docs/getting-started.md
+++ b/docs/getting-started.md
@@ -7,7 +7,7 @@ application you want to run. So, to run a complete blockchain that does
 something useful, you must start two programs: one is Tendermint Core,
 the other is your application, which can be written in any programming
 language. Recall from [the intro to
-ABCI](introduction.html#ABCI-Overview) that Tendermint Core handles all
+ABCI](./introduction.md#ABCI-Overview) that Tendermint Core handles all
 the p2p and consensus stuff, and just forwards transactions to the
 application when they need to be validated, or when they're ready to be
 committed to a block.
@@ -62,7 +62,7 @@ Tendermint before, use:
 If you have used Tendermint, you may want to reset the data for a new
 blockchain by running `tendermint unsafe_reset_all`. Then you can run
 `tendermint node` to start Tendermint, and connect to the app. For more
-details, see [the guide on using Tendermint](./using-tendermint.html).
+details, see [the guide on using Tendermint](./using-tendermint.md).
 
 You should see Tendermint making blocks! We can get the status of our
 Tendermint node as follows:
@@ -228,7 +228,7 @@ But if we send a `1`, it works again:
     }
 
 For more details on the `broadcast_tx` API, see [the guide on using
-Tendermint](./using-tendermint.html).
+Tendermint](./using-tendermint.md).
 
 ## CounterJS - Example in Another Language
 
diff --git a/docs/how-to-read-logs.md b/docs/how-to-read-logs.md
index 92f563cf..db808aca 100644
--- a/docs/how-to-read-logs.md
+++ b/docs/how-to-read-logs.md
@@ -53,8 +53,8 @@ Next follows a standard block creation cycle, where we enter a new
 round, propose a block, receive more than 2/3 of prevotes, then
 precommits and finally have a chance to commit a block. For details,
 please refer to [Consensus
-Overview](introduction.html#consensus-overview) or [Byzantine Consensus
-Algorithm](specification.html).
+Overview](./introduction.md#consensus-overview) or [Byzantine Consensus
+Algorithm](./spec/consensus).
 
     I[10-04|13:54:30.393] enterNewRound(91/0). Current: 91/0/RoundStepNewHeight module=consensus
     I[10-04|13:54:30.393] enterPropose(91/0). Current: 91/0/RoundStepNewRound module=consensus
@@ -100,7 +100,7 @@ Algorithm](specification.html).
 Here is the list of modules you may encounter in Tendermint's log and a
 little overview what they do.
 
--   `abci-client` As mentioned in [Application Development Guide](app-development.md#abci-design),    Tendermint acts as an ABCI
+-   `abci-client` As mentioned in [Application Development Guide](./app-development.md),    Tendermint acts as an ABCI
     client with respect to the application and maintains 3 connections:
     mempool, consensus and query. The code used by Tendermint Core can
     be found [here](https://github.com/tendermint/abci/tree/master/client).
@@ -115,13 +115,13 @@ little overview what they do.
     found
     [here](https://github.com/tendermint/tendermint/blob/master/types/events.go).
     You can subscribe to them by calling `subscribe` RPC method. Refer
-    to [RPC docs](specification/rpc.html) for additional information.
+    to [RPC docs](./specification/rpc.md) for additional information.
 -   `mempool` Mempool module handles all incoming transactions, whenever
     they are coming from peers or the application.
 -   `p2p` Provides an abstraction around peer-to-peer communication. For
     more details, please check out the
     [README](https://github.com/tendermint/tendermint/blob/master/p2p/README.md).
--   `rpc` [Tendermint's RPC](specification/rpc.html).
+-   `rpc` [Tendermint's RPC](./specification/rpc.md).
 -   `rpc-server` RPC server. For implementation details, please read the
     [README](https://github.com/tendermint/tendermint/blob/master/rpc/lib/README.md).
 -   `state` Represents the latest state and execution submodule, which
diff --git a/docs/using-tendermint.md b/docs/using-tendermint.md
index e645b48b..cd9545ef 100644
--- a/docs/using-tendermint.md
+++ b/docs/using-tendermint.md
@@ -130,7 +130,7 @@ new blockchain will not make any blocks.
 ## Configuration
 
 Tendermint uses a `config.toml` for configuration. For details, see [the
-config specification](./specification/configuration.html).
+config specification](./specification/configuration.md).
 
 Notable options include the socket address of the application
 (`proxy_app`), the listening address of the Tendermint peer
@@ -261,7 +261,7 @@ but must be positive, thus the range is: 0 through 9223372036854775807.
 Because of how the current proposer selection algorithm works, we do not
 recommend having voting powers greater than 10\^12 (ie. 1 trillion) (see
 [Proposals section of Byzantine Consensus
-Algorithm](./specification/byzantine-consensus-algorithm.html#proposals)
+Algorithm](./specification/byzantine-consensus-algorithm.md#proposals)
 for details).
 
 If we want to add more nodes to the network, we have two choices: we can
@@ -399,7 +399,7 @@ failing, you need at least four validator nodes (e.g., 2/3).
 
 Updating validators in a live network is supported but must be
 explicitly programmed by the application developer. See the [application
-developers guide](./app-development.html) for more details.
+developers guide](./app-development.md) for more details.
 
 ### Local Network