BACKGROUND: In Sub-Sahara Africa, malaria due to Plasmodium falciparum is the main cause of ill health. Evaluation of malaria interventions, such as drugs and vaccines depends on clinical definition of the disease, which is still a challenge due to lack of distinct malaria specific clinical features. Parasite threshold is used in definition of clinical malaria in evaluation of interventions. This however, is likely to be influenced by other factors such as transmission intensity as well as individual level of immunity against malaria. METHODS: This paper describes step function and dose response model with threshold parameter as a tool for estimation of parasite threshold for onset of malaria fever in highlands (low transmission) and lowlands (high transmission intensity) strata. These models were fitted using logistic regression stratified by strata and age groups (0-1, 2-3, 4-5, 6-9, and 10-19 years). Dose response model was further extended to fit all age groups combined in each stratum. Sub-sampling bootstrap was used to compute confidence intervals. Cross-sectional and passive case detection data from Korogwe district, north eastern Tanzania were used. RESULTS: Dose response model was better in the estimation of parasite thresholds. Parasite thresholds (scale = log parasite/microL) were high in lowlands than in highlands. In the lowlands, children in age group 4-5 years had the highest parasite threshold (8.73) while individuals aged 10-19 years had the lowest (6.81). In the highlands, children aged 0-1 years had the highest threshold (7.12) and those aged 10-19 years had the lowest (4.62). Regression analysis with all ages combined showed similar pattern of thresholds in both strata, whereby, in the lowlands the threshold was highest in age group 2-5 years and lowest in older individuals, while in the highlands was highest in age group 0-1 and decreased with increased age. The sensitivity of parasite threshold by age group ranged from 64%-74% in the lowlands and 67%-97% in the highlands; while specificity ranged between 67%-90% in the lowlands and 37%-73% in the highlands. CONCLUSION: Dose response model with threshold parameter can be used to estimate parasite threshold associated with malaria fever onset. Parasite threshold were lower in older individuals and in low malaria transmission area.