H1N1 refers to one type of influenza ('flu') virus. Often these originate in animals and are occasionally transmitted to humans. Swine flu (from pigs) or avian flu (from birds) has led to some of the epidemics in humans; other virus epidemics start from humans carrying the virus that can change its structure and start a new epidemic.
Vaccines made against the flu virus therefore need to be adapted almost every year to cope with these changes. The current flu vaccine contains 3 viruses, as recommended by the WHO for this coming flu season: an A/California/7/2009 (H1N1)-like virus, an A/Perth/16/2009 (H3N2)-like virus; and a B/Brisbane/60/2008-like virus.
For more information, go to the CDC web site below.