We compared the NPLALL statistic from GENEHUNTER with two-point and three-point MALODs and MFLODs from MFLINK for all autosomal markers in the Collaborative Study on the Genetics of Alcoholism (COGA) data set. In general MFLINK produced more significant results than GENEHUNTER and implicated two regions containing candidate genes (ADH3 and DRD2). Many regions of interest identified in other studies reported at this workshop produced MALODs significant at p < or = 0.05, but these would not have been picked up by GENEHUNTER unless a less significant threshold were used.