\documentclass[a4paper, 12pt]{article}

\begin{document}


\subsection{LaTeX comments}
This is a line with lilypond code
after the comment char % \lilypond{\context Voice <<c' e' g'>>}
% \lilypond{\context Voice <<c' e' g'>>}

If you do not see any music above
this line, then lilypond-book is handling latex comments pretty well :-)

The following snippet is preceded by a comment that would start a lilypond
environment

%%\begin{lilypond}
\begin{lilypond}[staffsize=11,fragment]
\context Voice <<c' e' g'>>
\end{lilypond}

A single-line comment inside a fragment does not confuse lilypond-book:

\begin{lilypond}[fragment]
c d e %\score
\end{lilypond}

\end{document}