There is a need for cell purification strategies suitable for handling small cell populations (tens to thousands of cells). We present here a novel strategy for small scale cell purifications using lectin-modified microchannels. Mammalian cells can be selectively captured in lectin-modified channels and eluted with a solution of the lectin's inhibiting sugar. As a proof-of-principle demonstration, two cell lines with different binding affinities to the lectin Sambucus nigra agglutinin (SNA) were combined at various ratios and introduced into SNA-modified microchannels. After incubation and washing, enrichments of approximately ten-fold were obtained for the SNA-binding cell type. The results demonstrate the potential of this miniaturized device for manipulation and purification of limited quantities of cells.