In May 2008 in the abortion amendments to the Human Fertilisation and Embryology Bill (now Act), Tony Cunningham voted for the abortion time limit to be lowered to 20 weeks against scientific and medical consensus which is currently 24 weeks. After four separate parliamentary votes on varying time limits, the majority of MPs voted to keep the abortion time limit at 24 weeks, in keeping with scientific and medical consensus, hence no abortion amendments were added to the bill.
In February 2015 Tony Cunningham voted against allowing mitochondrial donation, which would allow women who carried mitochondrial diseases to give birth to children who would not inherit the disease. If allowed, mitochondrial donation would be regulated by the Human Fertilisation and Embryology Authority (HFEA) meaning that there would be ongoing assessment of the safety and efficacy of such procedures. An October 2014 briefing report by the HFEA, which had been investigating the issue for three years, stated that there was no evidence to show that mitochondrial donation was unsafe. However, some religious groups had said that such procedures should not be allowed. The majority of MPs voted in favour of allowing mitochondrial donation.
In July 2010, Tony Cunningham signed four amended Early Day Motions critical of homeopathy: EDM 284A1: BMA Annual Representative Meeting Motions on Homeopathy, EDM 285A1: Effect of Homeopathic Remedies on Breast Cancer Cells, EDM 286A1: Homeopathic Medicines in the Treatment of Moderate to Severe Depression, and EDM 287A1: Homeopathy and Chronic Primary Insomnia. These amended motions were all against the use of homeopathy, and highlighted flaws in studies that had been welcomed by the original pro-homeopathy motions.
In September/October 2010, Tony Cunningham signed Early Day Motions 707: Government Funding for UK Science, and 767: Science is Vital Campaign. Both motions supported investment in science in the face of cuts anticipated in the coalition government's forthcoming spending review.