Embryonic development is highly sensitive to xenobiotic toxicity and in utero exposure to environmental toxins affects physiological responses of the progeny. In the US, the prevalace of allergic asthma is inexplicably rising and in utero exposure to cigarette smoke (CS) increases the risk of allergic asthma (AA) and bronchopulmonary dysplasia (BPD) in children and animal models. We reported that gestational exposure to sidestream (secondhand) CS (SS) promoted nicotinic acetylcholine receptor-dependent exacerbation of AA and BPD in mice. Recently, perinatal nicotine injections in rats were reported to induce peroxisome proliferator-activated receptor gamma (PPARγ)-dependent transgenerational transmission of asthma. Herein, we show that F1 and F2 progeny from gestationally SS-exposed mice exhibit exacerbated AA and BPD that is not dependent on the decrease in PPARγ levels. Lungs from these mice show strong eosinophilic infiltration, excessive Th2 polarization, marked airway hyperresponsiveness, alveolar simplification, decreased lung compliance, and decreased lung angiogenesis. At the molecular level, these changes are associated with increased RUNX3 expression, alveolar cell apoptosis, and the antiangiogenic factor GAX, and decreased expression of HIF-1α and pro-angiogenic factors NF-κB and VEGFR2 in the 7-day F1 and F2 lungs. Moreover, the lungs from these mice exhibit lower levels of micro-RNA (miR)-130a and increased levels of miR-16 and miR-221. These miRs regulate HIF-1α-regulated apoptotic, angiogenic, and immune pathways. Thus the intergenerational effects of gestational SS involve epigenetic regulation of HIF-1α through specific miRs contributing to increased incidence of AA and BPD in the progenies.