BACKGROUND: To evaluate the effect of two types of partial sleep deprivation (PSD) on biomarkers of muscle and cardiac injuries in response to acute intermittent exercise in professional athletes. METHODS: In a counterbalanced order, Ten healthy male Taekwondo athletes were asked to perform the Yo-Yo Intermittent Recovery Test (YYIRT) in three conditions, allowing a 36 h recovery period in between: i) following a full night of habitual sleep known as a reference sleep night (RN); ii) following PSD in the beginning of the night (PSDBN), and iii) following PSD in the end of the night (PSDEN). Heart rate (HR) and arterial oxygen saturation (SaO2) were measured during exercise. Blood samples were taken just before and 3 min after the YYIRT to measure biomarkers related to muscle and cardiac injuries. RESULTS: No significant effect of PSD was observed for physiological parameters (i.e., HR and SaO2). However, a significant alteration of resting ultra-sensitive C-reactive protein (P < 0.05) and myoglobin (MYO) (P < 0.01) levels was detected after PSDEN. Furthermore, all biomarkers related to muscle and cardiac injuries were altered by exercise. Likewise, compared to RN, PSD affected creatine phosphokinase and MYO levels in response to exercise (P < 0.05). CONCLUSION: The present study indicates that PSDEN increase the resting us-CRP and MYO levels, and that the two types of PSD increase the CPK and MYO levels in response to acute intermittent exercise, among Taekwondo athletes, in the evening of the following day. However, no rise of the physiological responses has been observed after the two types of PSD, at rest and in response to the exercise.