Malnutrition refers to the condition of nutrient imbalance, usually for a prolonged time. The imbalance can cause you to get too much of a given nutrient or too little. Undernutrition happens when a person doesn't get enough of any specific nutrient or all nutrients in general.
Usually when someone uses the word 'malnutrition,' they're referring to energy undernutrition, which is what happens when you don't get enough food to eat, or the food you have doesn't have enough protein or energy from protein, carbohydrates and fat.
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Gropper SS, Smith JL, Groff JL. "Advanced Nutrition and Human Metabolism." Fourth Edition. Belmont, CA. Wadsworth Publishing Company, 2005.
Smolin LA, Grosvenor, MB. "Nutrition: Science and Applications." Third Edition. Wiley Publishing Company, 2013.