With due respect I want to clearify that 234F is a "fees" and not penalty which is to be paid on or before itr and is applicable in cases of filing itr after applicable due date u/s139(1). It is irrespective of tax paid/payable or refundable in the return. Fees quantum is Rs. 1000/5000/10000 depending upon case to case. However the said fees is only applicable when the assessee has an obligation to file itr, which means if his/her total income before deductions under Chapter VI-A does not exceed the maximum amount not chargeable to tax viz. Rs. 250000, then section 234F is not applicable and hence no fees is to paid.