Incinerated medical waste residue has more heavy metals than municipal solid waste which if not well disposed of, could pollute the environment and pose a great danger to public health. A study was done on incinerators at Kenyatta National Hospital – Nairobi and Moi Teaching and Referral Hospital – Eldoret to assess levels of total chromium, cadmium, mercury, lead and silver from the bottom ash. Atomic absorption spectrophotometer was used for analysis. At KNH, incinerator bottom ash had mean concentrations of 5297, 140, 4299, 2092 and 57 mg/kg of total chromium, cadmium, lead, silver and mercury respectively. At MTRH, the concentrations in the ashes of 3870, 250, 4340, 1360 and 40 mg/kg of total chromium, cadmium, lead, silver and mercury were found. These exceeded the maximum limits specified by the Kenyan National Environmental Management Agency and European Union Standards for ordinary disposal. Regular quality monitoring of heavy metals in bottom ash of the two institutions’ incinerators to guide safe disposal of the residues was not practiced.