Mycoplasma gallisepticum (MG) is a major and economically significant pathogen of avian species. When administered before lay, F-strain MG (FMG) can reduce egg production during lay, but the ts-11 strain of MG (ts11MG) does not exert this effect. Two trials were conducted to determine the effects of pre-lay vaccinations of ts11MG, MG-Bacterin (MGBac), or their combination, in conjunction with an FMG vaccination overlay after peak production on the digestive and reproductive organ characteristics of Hy-Line W-36 layers housed in biological isolation units (4 units per treatment, 10 birds per unit). The following vaccination treatments were administered at 10 wk of age (woa): 1) Control (no vaccinations); 2) MGBac; 3) ts11MG; and 4) ts11MG and MGBac combination (ts11MG+MGBac). At 45 woa, half of the birds were vaccinated with a laboratory stock of high passage FMG. In both trials, parameters determined in 4 birds per unit at 55 woa included: BW; fatty liver hemorrhagic syndrome incidence; mean number of mature ovarian follicles; ovarian, oviduct, and small intestine weights; and the weights and lengths of the various portions of the oviduct and small intestine. Treatment effects were observed for the weights of the entire small intestine and the duodenum, jejunum, and ileum, as percentages of BW; and for vagina weight as a percentage of total oviduct weight. In general, the weights of the small intestine and its 3 components were increased in response to the FMG vaccine that was administered at 45 woa. An FMG vaccination at 45 woa may increase relative intestine weight in layers; however, use of a prelay MGBac vaccine alone or in combination with ts11MG, with or without an FMG overlay, does not affect the gross characteristics of their digestive and reproductive organs, and may be used without having an adverse effect on their performance, as was observed in a previous companion study.