MD with DOI

% All you need is text – Markdown (via pandoc) for academia
% Gerrit Hirschfeld^1^
% ^1^German Paediatric Pain Centre, Children’s Hospital Datteln, Germany


Address for correspondence: German Paediatric Pain Centre, Children’s and Adolescents’ Hospital Datteln, Dr.-Friedrich-Steiner Str. 5, 45711 Datteln, Germany; Tel.+49- 2363-975-183; Fax.+49- 2363-975-181; eMail:



Many students struggle to find an adequte format for their thesis. Ironically the advent of “modern” WYSIWYG programms seems to make it harder to consistently format a text.

While learning LaTeX may be a bit too much to ask for, markdown is a very minimal language that together with pandoc affords all typesetting needs for an academic paper. While the source document in markdown can be opened on any pc, pandoc can translate it into beautifully formatted pdf and docx (if it is absolutely necessary) files. Specifically markdown implements:

  • Headings, Subheadings
  • Figures and tables
  • Citations and References (here in APA6 but other styles are also possible)
  • You will need to edit the file

Once pandoc and latex is installed the following command generates the pdf

pandoc -s -S --biblio biblio.bib --csl apa.csl -N -V geometry:margin=1in -o paper.pdf  

What Markdown can do for you




and so forth




  • something
  • another thing
  1. or
  2. even
  3. numbered



Right Left Center Default
——- —— ———- ——-
12 12 12 12
123 123 123 123
1 1 1 1
Table: Demonstration of simple table syntax.


Example figure from one of my last papers


Pandoc supports the use of csl reference styles. That means that it is really easy to use comparatively complex conventions such as APA6. The figure is taken from [@textbfHirschfeld2013].

In order to change the reference style simply give another csl-file.

pandoc -s -S --biblio biblio.bib --csl apa.csl -N -V geometry:margin=1in -o paper.pdf

How you can make everthing else work

Advanced users can extend these using one or more of the following strategies:
– Use more LaTeX right in between the markdown
– Have a look at the pandoc options
– Use Pandoc to generate a tex-file first
– Use themes! Pandoc supports both LaTeX as well as docx themes.
– integrate your whoe dataanalysis into your markdown manuscript by using R and knitr.



This article and its reviews are distributed under the terms of the Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution, and redistribution in any medium, provided that the original author and source are credited.