Botswana is not your average African country. It is modern and developed and most things work. You can safely drink the tap water in towns and cities and you don't need protection against cholera or yellow fever.
HIV/AIDS is a serious issue but, unless you fail to take common sense precautions, there should be no undue risk. In fact, the greatest danger to the traveller is caused by wildlife and the inherent risks of driving in the bush.
The most significant concern for independent travellers is road safety. Botswana has one of the highest accident rates in the world, and drunk and reckless driving are common. Cattle, goats, sheep, donkeys as well as wild animals are deadly hazards on the road, especially at dusk and after dark when visibility is poor. To drive in Botswana you need to be prepared for the unexpected and observe the speed limits on unsurfaced roads.
If you are travelling in endemic areas it is extremely important to avoid mosquito bites and to take tablets to prevent this disease. Symptoms range from fever, chills and sweating, headache, diarrhoea and abdominal pains to a vague feeling of ill-health. Seek medical help immediately if malaria is suspected. Without treatment malaria can rapidly become more serious and can be fatal. If medical care is not available, malaria tablets can be used for treatment. You should seek medical advice, before you travel, on the right medication and dosage for you. If you do contract malaria, be sure to be re-tested for malaria once you return home as you can harbour malaria parasites in your body even if you are symptom free. Travellers are advised to prevent mosquito bites at all times. The main messages are: wear light-coloured clothing; wear long trousers and long-sleeved shirts; use mosquito repellents containing the compound DEET on exposed areas (prolonged overuse of DEET may be harmful, especially to children, but its use is considered preferable to being bitten by disease-transmitting mosquitoes); avoid perfumes and aftershave; use a mosquito net impregnated with mosquito repellent (permethrin) - it may be worth taking your own, and impregnating clothes with permethrin effectively deters mosquitoes and other insects.
40% of adults in Botswana are HIV+. HIV (Human Immuno-deficiency Virus) develops into AIDS (Acquired Immune Deficiency Syndrome), which is a fatal disease. Any exposure to blood, blood products or body fluids may put the individual at risk. The disease is often transmitted through sexual contact or dirty needles - body piercing, acupuncture, tattooing and vaccinations can be potentially as dangerous as intravenous drug use. HIV and AIDS can also be spread via infected blood transfusions, but blood supplies in most reputable hospitals are now screened, so the risk from transfusions is low. If you do need an injection, ask to see the syringe unwrapped in front of you, or take a needle and syringe pack with you. Fear of HIV infection should not preclude treatment for any serious medical conditions. Most countries have organizations and services for HIV-positive folks and people with AIDS. For a list of organizations divided by country, plus descriptions of their services, see www.aidsmap.com.