Ovaries from slaughtered cows are the most abundant source of preantral immature follicles for in vitro studies including maturation and in vitro fertilization. Integrity of immature follicles may be compromised by inadequate management during the collection and transport of the gonads, limiting the success of a correct evaluation. This study assessed the effect of aseptic and transport of bovine ovaries on the structural and ultrastructural integrity of immature follicles from the ovarian cortex. Ovaries from 20 different crossbred cows (Bos taurus × B. indicus) were randomly assigned to one of two aseptic and transport treatments: (1) the ovaries were washed once with 70 % ethanol for 10 s, rinsed twice with normal saline solution (OH + NSS), and then transported in NSS + 0.05 % gentamicin sulphate; or (2) the ovaries were washed three times with phosphate buffered saline (PBS) and transported in PBS + 0.05 % gentamicin sulphate. Samples of the ovarian cortex were obtained from each treatment group. Half of samples of each treatment was processed for histologic evaluation of follicular morphology and developmental stage using haematoxylin & eosin, and the other half was processed to analyse the ultrastructure of immature follicles using transmission electronic microscopy. The rates of good-quality follicles were 36.95 % and 88.6 % for OH + NSS and PBS, respectively. Histological analysis showed higher number of abnormal follicles in OH + NSS than in PBS treated ovaries (F 1,12 = 99.64, P = 0.0001). The proportions of morphological alterations were not significantly different between treatments (χ 2 1,7 = 7.72, P = 0.358). The ultrastructure of immature follicles from OH + NSS ovaries showed cell damage, revealed by abundant cell detritus around both, the oocyte and follicular cells. However, the presence of alterations was barely evident in both the cytoplasm and the nucleus of the granulosa cells.