Caffeine can affect muscle cell physiology and the inflammatory response during exercise. The purpose of this study was to analyse muscle damage markers and inflammatory cell infiltration into the soleus muscle of sedentary and exercised animals submitted to chronic caffeine intake. Thirty-two male Wistar rats were divided into the following four groups (n = 8 per group): sedentary control (SCO); sedentary + caffeine (SCAF); trained control (TCO); and trained + caffeine (TCAF). The animals were housed in individual cages and received tap water or caffeine (1 mg ml −1 ); they were maintained at rest or submitted to swimming for up to 40 min day −1 with a 4% load, five times per week for 30 days. Blood samples were collected for analysis of serum lactate, creatine kinase and calcium. The right soleus muscle and the epididymal fat depot were weighed, and the muscle was submitted to histological analysis. Training and caffeine did not change body or muscle weight, food and liquid intake or serum calcium levels among groups. Decreased fat tissue (P < 0.05) was observed in the SCAF (4.05 ± 1.03 g), TCO (4.14 ± 0.78 g) and TCAF groups (4.02 ± 1.02 g) compared with the SCO group (5.31 ± 1.06 g). Serum creatine kinase activity was significantly reduced in the SCAF (787.3 ± 230.3 U l −1 ), TCO (775.3 ± 232.3 U l −1 ) and TCAF groups (379.5 ± 110.5 U l −1 ) compared with the SCO group (1610.2 ± 276.5 U l −1 ). Few damaged muscle fibres (P < 0.05) were found in SCAF (16.7 ± 12.8%) and TCAF groups (17.3 ± 11.7%) compared with the SCO group (53.6 ± 13.9%). The SCAF group presented fewer fields with inflammatory cells (7.6 ± 8.7 fields) compared with the SCO group (123 ± 146 fields). The results suggest that the chronic intake of caffeine, as well as chronic low-intensity exercise, decreased muscle damage and inflammatory infiltration into skeletal muscle.