We have built a two laser flow cytometer for ultrasensitivefluorescence measurements. The instrument is used fortwo-parameter analysis of DNA fragments. Total DNAcontent of each fragment (proportional to its size) ismeasured using TOTO-1 excited at 514 nm. Specifictargets on the DNA are labeled with Cy5 and excited at647 nm. The sensitivity of the instrument allows thedetection of targets at the single molecule level. The signal-to-noise ratio for a single streptavidin-conjugated Cy5molecule (about four Cy5 molecules) is 7.5. The SNR fora single Cy5 molecule is 1.7.