We previously isolated cordycepin, guanosine and tryptophan from Cordyceps militaris as antiadipogenic constituents. For the quality control of C. militaris for anti-adipogenic activity, simultaneous analytical method using high-performance liquid chromatography (HPLC)-diode array detection (DAD) was developed and validated. Quantitation of these compounds in various Cordyceps samples from different sources and various extraction methods were conducted using developed method. Our study shows that natural Cordyceps and host insect possess higher content than cultured ones and fruiting bodies, respectively. The content of cordycepin showed great difference in different C. militaris samples whereas trytophan content was similar in tested samples. Addition of water to extraction solvent greatly increased the yield of guanosine and tryptophan. High temperature and longer extraction time increased yield of guanosine, whereas the content of trytophan was decreased in high temperature during extraction with water. Extraction using ultrasonic apparatus slightly increased extraction efficiency. Cordycepin, however, has little variation in different extraction method tested. Strong anti-adipogenic activity was observed in the samples that contain all the three constituents. Taken together, quantitation of these compounds using developed analytical method might provide basic requirement for the anti-adipogenic activity of C. militaris.