A comparison of university lecturers’ perception towards consumption of genetically modified foods in Nigeria and Botswana was conducted in 2007. Simple random sampling technique was used to select 100 lecturers out of 685 from five faculties of agriculture in south western Nigeria and 47 from 67 in Botswana College of Agriculture (BCA). Data were collected through structured questionnaire on demographic characteristics and perception on consumption of genetically modified (GM) foods containing 15 statements that cut across situations in Nigeria and Botswana; and analyzed using means and standard deviation. Mann Whitney U test was used to compare the perception of lecturers in the two countries. The results showed that majority were males (77 and 57 percent respectively), with 51 percent of the lecturers in Botswana between the 51–60 years and 59 percent between 41–50 years in Nigeria. The percentage of lecturers in Botswana that are MSc degree holders (45 percent) was higher than those from Nigeria. Lecturers from BCA agreed and were positively disposed to 12, while lecturers from south western universities in Nigeria agreed and are positively disposed to five out of the 15 statements on the rating scale. It is important to note that four of the statements were perceived positively by lectures from both countries. Also, significant difference existed in their perception (Z = –6.65, p < 0.05); with higher mean rank for Botswana (108.02) than for Nigeria (58.01). This further confirms that Botswana lecturers are more favorably disposed to genetically modified foods than Nigeria lecturers.