Proteomic approaches are increasingly being used to complement genetic and RNA interference-based studies of gene function in Caenorhabditis elegans. Several strategies to isolate protein complexes from whole worms and individual differentiated cell types have been described. In vivo labelling methods have also been developed to quantitatively assess proteome-wide changes depending on genetic composition or developmental stage. Here, we review proteomic approaches that are becoming part of the essential toolbox for studies of gene function in C. elegans and highlight specific examples where their application has led to important new insights.