There are a number of problems that can lead to a vitamin B12 or folate deficiency, including: pernicious anaemia – where your immune system attacks healthy cells in your stomach, preventing your body from absorbing vitamin B12 from the food you eat; this is the most common cause of vitamin B12 deficiency in the UK a lack of these vitamins in your diet – this is uncommon, but can occur if you have a vegan diet, follow a fad diet or have a generally poor diet for a long time medication – certain medications, including anticonvulsants and proton pump inhibitors (PPIs), can affect how much of these vitamins your body absorbs