This study investigated gender, caponization and exogenous estrogen effects on lipids, bone and blood characteristics in Taiwan country chickens. Thirty male chickens were caponized at 8 weeks (capons); 15 capons were injected with estrogen (5 mg/bird estradiol 3-benzoate) every 2 weeks from 8 to 28 weeks, and 15 sham-operated male (shams) chickens and 15 females were selected for this trial. The results showed that the shams had lower relative abdominal and chest subcutaneous fat than females (P < 0.05). The estrogen-treated capons had greater relative abdominal and chest subcutaneous fat than shams and capons (P < 0.05), which might result from higher blood very low-density lipoproteins and triacylglycerol concentrations (P < 0.05). Caponization could dramatically increase relative abdominal fat (506%; P < 0.05). The shams had higher tibia weight and biomechanical properties, such as maximum bone strength and bending moment values than the capons (P < 0.05). Tibia biomechanical properties were reduced by estrogen treatment (P < 0.05). The females obtained the lowest biomechanical value in all treatments (P < 0.05). Histological examination revealed cavity formation in the cortical bone of estrogen-treated capons and female chickens, which suggested that estrogen reduced bone biomechanical properties by destroying its structural integrity.