The incidence and potential determinants of tick borne diseases (TBDs) were estimated in a longitudinal study that was conducted in cohorts of youngstock animals of less than 3 years kept in smallholder dairy farms in Tanga region, Tanzania. A combination of serological tests, blood and lymph node smears were used as diagnostic tests for TBDs during the study. A total number of 549 youngstock were followed for a total of 532.2 animal years from August 1999 to July 2001. Overall morbidity and mortality rates (due to all causes) were 8.26 and 12.0 per 100 animals year at risk, respectively. Of the total deaths, 56% were attributed to TBDs (37.5%-East Coast fever (ECF) and 18%-anaplasmosis). Specific morbidity and mortality rates for ECF were estimated to be 3.57 and 4.51 per 100 animals year risk, respectively, and for anaplasmosis 2.21 and 2.25 per 100 animals year risk, respectively. Analysis of survival times to death indicated that calves < 6 months of age and those out on pasture had higher death rates than older calves and those kept under zero-grazing systems (relative risk [RR] 3.80, P = 0.001 for pasture-grazed calves). There was no mortality or morbidity arising specifically from cowdriosis (heartwater) or babesiosis during the whole period of monitoring. The study revealed that most farms were applying under strength acaricide and using acaricides at irregular intervals. It is concluded that TBDs namely ECF and anaplasmosis are important diseases in this farming system and reducing morbidity and mortality in smallholder dairy farms in Tanga region is an achievable goal. Both farmers and extension services should target at risk calves with the provision of both strict tick control and optimal husbandry management practices.