Counting has begun at four centers of Porbandar, Panchmahal, Limbadi and Banaskantha for all the seats and results are expected by the afternoon, officials said.
Early trends, during the first hour of the counting, suggest that on two Lok Sabha and three Assembly seats, BJP candidates were leading against their nearest Congress rivals.
"BJP candidates are leading in two Lok Sabha seats of Porbandar and Banaskantha and three Assembly seats of Jetpur, Limbadi and Dhoraji," a top state Election official said.
The bye-election are considered as a litmus test for Congress as all six seats were held by it.
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Both the main political parties in the state, ruling BJP and opposition Congress have expressed confidence of winning majority of seats even though this bye-elections did not enthuse the voters much.
For Porbandar and Banaskantha Lok Sabha seats, 30 and 37 per cent voting was registered respectively. However, for the assembly seats of Limbadi, Morva Hadaf, Dhoraji and Jetpur 62 per cent, 64 per cent, 33 per cent and 45 per cent voting was recorded.
On Limbadi and Morva Hadaf Assembly and Banaskantha Lok Sabha seat, Congress had fielded relatives of candidates who held those seats before the bypoll.