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I saw mention of this study in a number of places - that low vitamin D levels are linked to chronic headaches. A little too soon to know if that is really true -  the researchers in this study looked at the blood vitamin D levels of 2601 men just one time, and did not give vitamin D supplements to the men to see if this changed the frequency of migraine headaches. The researchers themselves pointed out that other studies looking at this same issue have had mixed results. And they themselves pointed out that low blood levels of vitamin D (serum 25(OH)D concentration) was associated with a markedly higher risk of frequent headache in men. Associated does not mean caused.

Yes, low vitamin D levels is linked to a number of health problems (see all vitamin D posts). But at this point I think that it's a case of "wait and see" to see if vitamin D levels have something to do with headache frequency. Perhaps other micronutrients are important, perhaps something else. Note that in the study they used below 50 nmol as the measure for low vitamin D levels. In the USA, that translates into below 20 ng/ml, which everyone agrees is too low (a deficiency). The best source of vitamin D is sunlight - which is why it's called the "sunshine vitamin". From Science Daily:

Vitamin D deficiency increases risk of chronic headache

Vitamin D deficiency may increase the risk of chronic headache, according to a new study from the University of Eastern Finland....The Kuopio Ischaemic Heart Disease Risk Factor Study, KIHD, analysed the serum vitamin D levels and occurrence of headache in approximately 2,600 men aged between 42 and 60 years in 1984-1989. In 68% of these men, the serum vitamin D level was below 50 nmol/l, which is generally considered the threshold for vitamin D deficiency. Chronic headache occurring at least on a weekly basis was reported by 250 men, and men reporting chronic headache had lower serum vitamin D levels than others.

When the study population was divided into four groups based on their serum vitamin D levels, the group with the lowest levels had over a twofold risk of chronic headache in comparison to the group with the highest levels. Chronic headache was also more frequently reported by men who were examined outside the summer months of June through September. Thanks to UVB radiation from the sun, the average serum vitamin D levels are higher during the summer months.

The study adds to the accumulating body of evidence linking a low intake of vitamin D to an increased risk of chronic diseases. Low vitamin D levels have been associated with the risk of headache also by some earlier, mainly considerably smaller studies.