In obstructive sleep apnea syndrome (OSAS) hypoxia and sleep deprivation lead to neuropsychological impairments. Our goal in this study to evaluate working memory and skill learning to get a complex picture about cortical and sub-cortical function in patients with sleep apnea. Twenty-one OSAS patients and 21 healthy controls participated in the study. We analyzed verbal-, vizuo-spatial, complex working memory, general skill learning and sequence specific learning separately. Our data show that complex working memory was impaired in OSAS patients, in contrary OSAS patients represented better achievement in the vizuo-spatial task compared to the control group. We found that OSAS patients showed general skill learning and implicit learning of probabilistic sequences similar to that of controls. Taken together, we found dissociation between working memory and implicit sequence learning in OSAS. These findings suggest that sleep has less influence on the functions related to sub-cortical structures like cortical functions.