The research in the area of health sciences students’ sleep quality and mood disorders is lacking in Lithuania, as well as other European countries. The aim of this study was to compare prevalence of poor sleep, anxiety and depression among the students according to the study programmes and to assess the relations among poor sleep, depression and anxiety. The study sample consisted of 672 Klaipeda State University of Applied Sciences students (95.5% were female), from 18 to 46 years of age. Sleep quality was evaluated by Pittsburgh Sleep Quality Index, anxiety by Hospital Anxiety and Depression Scale, sociodemographic questions were used. The chi-square test or Fisher exact test was used to estimate association between categorical variables. P-values less than 0.05 were interpreted as statistically significant. Poor sleep was more prevalent among Beauty Therapy (26.4%, 95% CI 22.2-30.56) and Nursing (21.3%, 95% CI 17.42 – 25.17) students, as compared with persons studying in Oral Health programmes (14.8%, 95% CI 11.46 – 18.17), p<0.05. Depression mean score was higher in Beauty Therapy students (4.76), as compared to Oral Health (3.69) students, p<0.05. Beauty Therapy (9.99) or Physiotherapy students (8.24) had higher anxiety mean score, as compared to Oral Health students (7.14), p<0.05. Anxiety mean score was significantly higher (8.45) among the ones with disturbed sleep, as compared to normally sleeping students (5.86), p<0.001. Depression mean score (4.77) was higher among the students having disturbed sleep, as compared to the students which sleep was not disturbed (2.87), p<0.001. Poor sleep and anxiety were more prevalent among the students aged 20 years and older as compared to the students, aged 18 and 19 years. Second and third year students more often had poor sleep or anxiety as compared to the first-year students. Poor sleep and anxiety were more common among Beauty Therapy and Physiotherapy students than among Oral Health Students. Among the students who slept poorly, symptoms of anxiety and depression were statistically significantly more frequent than those students whose sleep was not disturbed. Depression and anxiety mean scores were statistically significantly higher among the students who had poor sleep, as compared to the ones who had normal sleep, in all age and year of studying groups.