Chia seeds were utilized by Aztecs as food and for medicinal purposes. Nowadays, this crop is gaining importance in many countries, due to its nutritional attributes. Some physical properties and chemical characteristics of chia seeds from four different regions of Mexico were evaluated and compared. Seed size distribution was not significantly affected (P > 0.05) by the region, with similar values of seed length (2.03–2.10 mm), width (1.27–1.32 mm), thickness (0.77–0.81 mm) and surface area (4.95–5.42 mm2). Bulk density (662–741 kg m−3), geometry and granulometric distribution were also determined. Origin of tested seeds significantly (P < 0.05) influenced their composition; all seeds had high contents of protein (18.5–22.3%), fat (21.5–32.7%) and fibre (20.1–36.1%). Chia seeds ratio between omega-3 and omega-6 fatty acids was 3:1 for the studied regions; seeds from Chiapas and Michoacán had the highest proportion of ω-6 and ω-3 fatty acids. The studied seeds contained phenolic compounds in the range of 0.53–0.71 mg GAE g−1.