Abstract-Larval and juvenile shortnose {Chasmistes brevirostris) and Lost River (Deltistes luxatus) suckers from Upper Klamath Lake, OR, were examined to determine anomaly rates for fins, eyes, spinal column, vertebrae, and osteocranium, and their possible associations with water quality and pesticides. X-rays of 1,550 fish and 1,395 matching specimens, collected in 1993, were ranked on the severity of anomalies. One or more anomalies were observed in 15.9% of shortnose suckers and 8.2% of Lost River suckers. Anomaly rates exceeding 1.0%, greater than rates expected from high water quality systems, were observed for lordosis and scoliosis, and abnormalities of the vertebrae, opercula, and pectoral and pelvic fins in shortnose suckers, and abnormalities of vertebrae and opercula in Lost River suckers. The highest rates of anomalies were in vertebrae, pelvic fins, and opercula in shortnose suckers, and opercula and vertebrae in Lost River suckers. Shortnose suckers exhibited higher rates than Lost River suckers for almost all anomalies. Particular anomaly rates differed significantly among sites. There were also substantially more anomalies found in larvae and small juveniles than in larger juveniles. Based on the high anomaly rates observed in this study, it is possible that 0-aged sucker cohorts in Upper Klamath Lake are far more vulnerable to mortality.