Endogenous circadian rhythmicity and sleep-wake homeostasis are robust regulators of human alertness and performance, yet few studies have examined how these regulatory processes affect motivation. Moreover, the influence of alertness and motivation on performance, independent of circadian phase and hours awake, has not been studied. Healthy subjects, 12 males and 3 females, ages 20 to 41, participated in a 2-week 28-h forced desynchrony protocol to address these issues. Subjects performed a battery of tests every 2 hours during scheduled wakefulness. Performance on a mathematical addition test and ratings of alertness and motivation on visual analog scales were analyzed. Performance scores were categorized as being associated with the highest or lowest alertness and motivation ratings for each circadian phase/hours awake bin to determine whether high levels of alertness and motivation resulted in higher performance scores above and beyond the effects of circadian and homeostatic regulation. Motivation varied significantly as a function of circadian phase and hours awake. Motivation and alertness were correlated. When circadian phase and hours awake were accounted for, performance was better when alertness and motivation ratings were highest and worse when those ratings were lowest. The present findings suggest that human performance is influenced by alertness and motivation independent of circadian phase and hours awake. Future studies examining the influence of circadian phase and sleep-wake homeostasis on human performance also should assess alertness and motivation to aid in the interpretation of performance data. Such studies also may aid in the development of countermeasures to improve human performance.