Objectives: The aim of the study was to investigate the trends in the incidence of occupational diseases in Lithuania during the period of 1999-2008. The analysis concerned both the individuals with diagnosed disease(s) and the number of diagnosed cases. Material and Methods: Incidence rates were calculated using data from the Republic of Lithuania National Register of Occupational Diseases and data on the employed population provided by the government Department of Statistics. The rates were age-standardized using the direct standardization method. The changes in the incidence rates throughout the study period were analyzed using segmented regression calculated with the JOINPOINT (v. 3.3.1) statistical software. We determined joinpoints in the dynamic lines of the incidence rates and calculated mean annual absolute change and mean annual relative (percentage) change for each period. Results and Conclusions: During the study period, the number of occupational diseases was, on average, 1.5 times as high as the number of individuals diagnosed with such diseases. Joinpoint positions in the dynamic lines of the incidence rates coincided for individuals with occupational diseases and for the cases of occupational diseases. The incidence was found to slightly increase during the period of 1999-2003, then to rise more rapidly during that of 2003-2006, and to decrease from 2006 to 2008.