Heat stress is an increasing challenge to the sustainability of poultry production in the tropics due to global warming. This study determined the effect of posthatch thermal conditioning on heat stress indices, haematological parameters and expression of brain derived neurotrophic factor (BDNF) gene in three meat type chickens; Cobb 500 (C500), Ross 308 (R308) and improved Nigerian indigenous broiler - FUNAAB Alpha (FA). The interplay of individual bird’s genetics and thermal treatment at critical periods on thermoregulation was largely unpublished as at the time this study was conducted. Thermal conditioning was carried out on day 6 by exposing 20 chicks from each strain to high temperature of 40±1 °C for 3 hours. Both conditioned and unconditioned chicks were exposed to acute heat challenge of 40±1 °C for 15 minutes on day 10. Blood samples were collected to determine haematological parameters. Tissue samples were collected from which RNA were extracted, synthesized into cDNA and subjected to qPCR. Strain and thermal conditioning interaction was significant (p<0.05) on haematological parameters with conditioned C500 having the highest means for packed cell volume, haemoglobin and red blood cell counts. Interactive effect was also significant (p<0.05) on BDNF gene expression, with conditioned FA having the highest. The study concluded that variation in traits due to thermal treatment is strain-specific and thermal conditioning is recommended for commercial broilers in southwestern Nigeria.