To bear in mind is to be mindful of or consider something. When you bear in mind the fact that your friend is scared of heights, you won't suggest a ride on a huge Ferris wheel.
Your doctor might give you a clean bill of health, adding, "Bear in mind that you've been sick, and take it easy for a while." When you're babysitting, you might promise the parents that you'll bear in mind the fact that their kids go crazy if they eat sugar. In either case, you're keeping a fact or an idea in your thoughts. This phrase combines the "carry or hold" meaning of bear with an old fashioned sense of mind — "memory."