This study reports on variation in the yields of N-nitrosonornicotine (NNN) and (4-methylnitrosoamino)-1-(3-pyridyl)-1-butanone (NNK) from the mainstream smoke of cigarette brands and describes factors affecting this variation. Yields of NNN and NNK from smoke and tobacco filler, which is blended and cut tobacco filled in a cigarette tube, together with cigarette design parameters, were measured for 11 commercial cigarette brands, which were available in Japan from 2009 to 2013. The ranges of the relative standard deviations (RSDs) for NNN from the smoke of each brand were 5.0%–29.9% under International Organization for Standardization (ISO) and 6.3%–26.3% under Health Canada Intense (HCI) smoking regime. When these RSDs were compared with those of tar, nicotine, and carbon monoxide yields in each brand, they were found to be much higher for all of the brands under the HCI, and higher for most of the brands under the ISO smoking regime. In addition, the RSDs of NNN and NNK in smoke were mostly higher than those of KY3R4F which was manufactured in a single batch. It was identified that variation in NNN yields from tobacco filler mainly contribute to variation in NNN yields from smoke.