I have been standing for about a year. As far as I can tell there are no bad effects from standing. It does take time to build the stamina to stand constantly for a day, but that is just a matter of temporary fatigue while your stamina improves. Once your stamina is to the point that you can stand all day every week, there are no downsides as far as I can tell.
It's important to ergonomically adjust your desk so that it's in the correct position, of course. Stand normally with your arms limp at your sides. Now, without moving your elbows, bring your hands up such that your forearms are horizontal, hands straight in front of you. Your hands now indicate where your keyboard should be -- roughly an inch or two below your elbow. Your mouse should also be reachable from that position without moving your elbow.
It's important to ergonomically adjust your desk so that it's in the correct position, of course. Stand normally with your arms limp at your sides. Now, without moving your elbows, bring your hands up such that your forearms are horizontal, hands straight in front of you. Your hands now indicate where your keyboard should be -- roughly an inch or two below your elbow. Your mouse should also be reachable from that position without moving your elbow.