Body condition index is used as a measure for an individual's condition, usually with reference to its nutritional status and the energy reserves. Reproductive success, survival, and thus, population dynamics, depend on body condition of the organisms. In this study, the seasonal and annual body condition factor (a) and the relative body condition index (Krel) were estimated from the length–weight relationship of green turtles (Chelonia mydas) collected in 3 coastal lagoons of Baja California Sur during 2005–2007. Seasonal and annual differences in a, and differences between study sites and physical appearance (healthy or injured) of Krel were analyzed. Juveniles were the predominant age class (< 77 cm straight carapace length). Green turtles from Punta Abreojos (PAO) had a lower Krel than individuals of Laguna San Ignacio at a given size. In Bahía Magdalena (BMA) and PAO injured green turtles had a smaller Krel than turtles classified as healthy at a given size. Additionally, the increase in Krel per cm of straight carapace length of injured green turtles from PAO was lower than that of healthy ones. Body condition factor, a, varied between years in turtles from PAO, being highest during 2006. An increasing tendency in a, from winter to summer, was observed in PAO and BMA. The periods when green turtles had the highest body condition factor a (summer, 2005 BMA, 2006 PAO) coincided with periods of highest serum concentrations of glucose, proteins, lipids, calcium, and uric acid; nevertheless, the relative body condition index was not correlated with those parameters. The relative body condition index resulted in a simple and sensible method that provided an overall trend of the data under a number of stress conditions, detecting differences also between injured and healthy individuals. The body condition factor, in conjunction with blood biochemistry parameters, proved to be a useful tool as biomarkers of the apparent physical and nutritional status of the green sea turtles.