The most common medical problem will be traveler’s diarrhea.  This can be caused by two very different reasons: 'harmless' amoeba in drinking water (which does cause diarrhea for the first few days....if however you are visiting for more than two weeks, drinking tap water will cause initial diarrhea, then it will go with no medication when your body is used to this type of amoeba); the other are quite harmful bacteria from not properly washed food (salads, fruit juices, etc...) Here is what you need to do to avoid it:

• Bottled water at all times...no exception
• Used bottled water for brushing of your teeth.
•  Be careful not to swallow water when taking a shower
• Tea/coffee is OK as long as long as the water has been boiled
• Avoid ice since it is most probably from tap water (see comment above)
• Do not eat street food or restaurants that are not frequented by Westerners (even that is not a guarantee)
• Stay away from salads
• Do not eat the food on the trains
• Lime juice is an excellent natural disinfectant. So it is a good idea to buy some limes (vegetable sellers or supermarket), wash them and have them with you. If in doubt of anything that you are going to be eating or drinking (including water or drinks with ice) cut the limes and squeeze one or two on what you are going to consume. Have used this trick and it never failed. 
• Always be sure to keep a good hand hygiene. Buy disinfectant gel and use it often.

It is not always the food or drinking water causing upset stomach or diarrhea: touching the Egyptian money and putting your finger into your mouth will transfer a load of bacteria into your body.

 Here is list of medications you must take with you:

• Rehydration salts
• Cipro
• Imodium
• Thermometer
  

If you do get sick, here is what you should do:

• Drink plenty of bottled water and use those rehydration salts
• If you do not have rehydration salts, mix salt, sugar and water together and drink it.   Plain water usually does not get absorbed by your body if you are suffering from diarrhea. The salt and sugar will help with the absorption and also replenish the lost minerals.
• Squeeze a couple of limes and drink the juice concentrated with no water a few times a day. It will act as a disinfectant, and also will decrease the diarrhea.
• If there is a need, take disinfecting medication (e.g. Intetrix which is available over the counter at any pharmacy) 
• If the diarrhea is very bad, a 'natural' way to stop it is to have black coffee with lime juice in it.
• Avoid very cold water.
• Most hotels can call a doctor for you.  Egyptian doctors tend to over medicate but if you are really dehydrated, they can give IV fluids. 

or ask if someone (e.g. hotel staff, or holiday rep.) can get you some 'DROTAZIDE' which is much more effective than Immodium, and only seems to be available in Egypt.

You can also seek medical advice before travelling to Egypt. Some doctors can offer a vaccination against cholera, which as a "side-effect" also protect you against traveller's diarrhea. This vaccination is quite expensive.