Malabsorption isย difficulty in the digestion or absorption of nutrients from food. Malabsorption can affect growth and development, or it can lead to specific illnesses.ย Many diseases can cause malabsorption. Most often, malabsorption involves problems absorbing certain sugars, fats, proteins, or vitamins. It can also involve an overall problem with absorbing food. Problems or damage to the small intestine that may lead to problems absorbing important nutrients. When you eat a healthy meal, you expect your body to reap the benefits of the vitamins and minerals. But a condition called malabsorption syndrome means your body isn't able to take in many of the nutrients from the food you eat. This digestive problem can lead to symptoms such as bloating and diarrhea.