Purpose This study aimed to identify and describe the time course of tolerance to the most common caffeine-induced side effects. Methods Eleven participants took part in a crossover, double-blind placebo-controlled experimental design. In one phase, participants ingested 3 mg/kg/day of caffeine for 20 days, while in another phase, they ingested a placebo. Resting heart rate and blood pressure were measured three times per week during each 20-day phase and a quantitative survey was used to categorise the magnitude of side effects. Results In the pairwise comparison with the placebo, the ingestion of caffeine increased systolic (+ 7.8 +/- 10.1%,P < 0.05) and diastolic blood pressure (+ 6.4 +/- 12.9%P < 0.05) for the first 8 days of ingestion, but then this effect became attenuated for both outcomes (on day 20, - 1.1 +/- 4.3% and + 0.9 +/- 9.6%, respectively). The ingestion of caffeine did not affect heart rate at any time point. Caffeine increased the feelings of nervousness and vigour and the rating of gastrointestinal complaints, insomnia and diuresis at several time points in the treatment (P < 0.05) and they did not disappear after 20 days of ingestion. Conclusions The daily intake of 3 mg/kg of caffeine induced a meaningful elevation in arterial blood pressure that disappeared after 8 days. However, other caffeine-induced effects such as increased nervousness and vigour, irritability, insomnia and diuresis remained after 20 days of consecutive caffeine ingestion. Although there was clear tolerance to the effect of caffeine on blood pressure, the persistence of other side effects suggests the inconvenience of maintaining a chronic caffeine intake, at least at the dose of 3 mg/kg/day.