diff --git a/app/coffee/LatexRunner.coffee b/app/coffee/LatexRunner.coffee
index 8f032cd..a35ae0b 100644
--- a/app/coffee/LatexRunner.coffee
+++ b/app/coffee/LatexRunner.coffee
@@ -12,9 +12,9 @@ module.exports = LatexRunner =
 
 		logger.log directory: directory, compiler: compiler, timeout: timeout, mainFile: mainFile, "starting compile"
 
-		# We want to run latexmk on the tex file which we it will automatically
-		# generate from the Rtex file.
-		mainFile = mainFile.replace(/\.Rtex$/, ".tex")
+		# We want to run latexmk on the tex file which we will automatically
+		# generate from the Rtex/Rmd/md file.
+		mainFile = mainFile.replace(/\.(Rtex|md|Rmd)$/, ".tex")
 
 		if compiler == "pdflatex"
 			command = LatexRunner._pdflatexCommand mainFile
diff --git a/test/acceptance/fixtures/examples/markdown-included/chapters/chapter1.md b/test/acceptance/fixtures/examples/markdown-included/chapters/chapter1.md
new file mode 100644
index 0000000..920d9be
--- /dev/null
+++ b/test/acceptance/fixtures/examples/markdown-included/chapters/chapter1.md
@@ -0,0 +1,17 @@
+Section Title
+-------------
+
+* List item one
+* List item two
+
+: Sample grid table.
+
++---------------+---------------+--------------------+
+| Fruit         | Price         | Advantages         |
++===============+===============+====================+
+| Bananas       | $1.34         | - built-in wrapper |
+|               |               | - bright color     |
++---------------+---------------+--------------------+
+| Oranges       | $2.10         | - cures scurvy     |
+|               |               | - tasty            |
++---------------+---------------+--------------------+
diff --git a/test/acceptance/fixtures/examples/markdown-included/main.tex b/test/acceptance/fixtures/examples/markdown-included/main.tex
new file mode 100644
index 0000000..bfda962
--- /dev/null
+++ b/test/acceptance/fixtures/examples/markdown-included/main.tex
@@ -0,0 +1,9 @@
+\documentclass{article}
+\usepackage{longtable}
+\usepackage{booktabs, multicol, multirow}
+
+\begin{document}
+
+\input{chapters/chapter1}
+
+\end{document}
diff --git a/test/acceptance/fixtures/examples/markdown-included/output.pdf b/test/acceptance/fixtures/examples/markdown-included/output.pdf
new file mode 100644
index 0000000..81a1136
Binary files /dev/null and b/test/acceptance/fixtures/examples/markdown-included/output.pdf differ
diff --git a/test/acceptance/fixtures/examples/markdown-standalone/main.md b/test/acceptance/fixtures/examples/markdown-standalone/main.md
new file mode 100644
index 0000000..036d971
--- /dev/null
+++ b/test/acceptance/fixtures/examples/markdown-standalone/main.md
@@ -0,0 +1,23 @@
+% Title
+% Author
+% Date
+
+Chapter title
+=============
+
+Section Title
+-------------
+
+Hello world. Have a nice table:
+
+: Sample grid table.
+
++---------------+---------------+--------------------+
+| Fruit         | Price         | Advantages         |
++===============+===============+====================+
+| Bananas       | $1.34         | - built-in wrapper |
+|               |               | - bright color     |
++---------------+---------------+--------------------+
+| Oranges       | $2.10         | - cures scurvy     |
+|               |               | - tasty            |
++---------------+---------------+--------------------+
diff --git a/test/acceptance/fixtures/examples/markdown-standalone/output.pdf b/test/acceptance/fixtures/examples/markdown-standalone/output.pdf
new file mode 100644
index 0000000..9991ab8
Binary files /dev/null and b/test/acceptance/fixtures/examples/markdown-standalone/output.pdf differ