Filariasis caused by Brugia timori and Wuchereria bancrofti is an important public health problem on Alor island, East Nusa Tenggara, Indonesia. To implement a control programme, adverse reactions and short-term effects on the microfilaria (mf) density were studied following a divided dose of diethylcarbamazine (DEC, 6 mg/kg body weight – 100 mg on day 1 and the rest on day 3) or a single dose of DEC (6 mg/kg body weight on day 3) and albendazole (Alb, 400 mg). In order to define the most appropriate regimen, 30 persons infected with B. timori were treated in the hospital and results were compared with those obtained from the treatment of 27 persons infected with W. bancrofti. Adverse reactions consisted of systemic reactions such as fever, headache, myalgia, itching and local reactions such as adenolymphangitis. Fever experienced by a number of patients in both treatment groups generally occurred 12–24 h after drug administration and lasted up to 2 days. Adenolymphangitis tended to occur later and was resolved within 4 days. The number of W. bancrofti patients suffering from adverse reactions was lower and the reactions were milder than those of the B. timori patients. There was no difference in adverse reactions between DEC alone and DEC–Alb treatment for either infection. The geometric mean mf count decreased on day 7 in the B. timori infected patients from 234 mf/ml in the DEC group and from 257 mf/ml in the DEC–Alb group to 7 and 8 mf/ml, respectively. The mf densities of the W. bancrofti infected patients decreased on day 7 from 214 mf/ml in the DEC group and from 559 mf/ml in the DEC–Alb group to 15 and 14 mf/ml, respectively. Our data indicate that the microfilaricidal effect of the drugs is achieved more rapidly for B. timori, which is associated with more adverse reactions than W. bancrofti. In addition, 111 B. timori infected persons were treated in the community with DEC–Alb in one selected village. The adverse reactions and the reduction of mf density was similar to the findings of the hospital-based study. In this group, there was a strong correlation of mf density with the frequency and severity of adverse reactions. The addition of Alb resulted in no additional adverse reactions compared with DEC treatment alone and can also be used for the treatment of B. timori infection. In Indonesia, where the prevalence of intestinal helminths is high, the use of a combination of DEC and Alb to control lymphatic filariasis may also have impact on the control of intestinal helminths.